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Issue 16, 2012
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Assigning kinetic 3D-signatures to glycocodes

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Reconciling glycocodes and their associated bioactivities, via 3D-structure, will rationalise burgeoning high-throughput functional glycomics data and underpin a new era of opportunity in chemical biology. A major impasse to achieving this goal is a detailed understanding of pyranose sugar ring 3D-conformation (or pucker) and the affiliated microsecond-timescale exchange kinetics. Here, we perform hardware-accelerated kinetically-rigorous equilibrium simulations of fundamental monosaccharides to produce the hypothesis that pyranoses have microsecond-timescale kinetic puckering signatures in water, classified as unstable (rare in the glycome), metastable (infrequently observed) and stable (prevalent). The predicted μs-metastability of β-D-glucose explained hitherto irreconcilable experimental measurements. Twisted puckers seen in carbohydrate enzymes were present in the aqueous 3D-ensemble (suggesting preorganization) and pyranose-water interactions accounted for the relative stability of β-D-galactose. Characteristic 3D-shapes for biologically- and commercially-important carbohydrates and new rules linking chemical modifications with pyranose μs-puckering kinetics are proposed. The observations advance structural-glycomics towards dynamic 3D-templates suitable for structure-based design.

Graphical abstract: Assigning kinetic 3D-signatures to glycocodes

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The article was received on 09 Jan 2012, accepted on 23 Feb 2012 and first published on 23 Feb 2012

Article type: Paper
DOI: 10.1039/C2CP40071E
Citation: Phys. Chem. Chem. Phys., 2012,14, 5843-5848
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    Assigning kinetic 3D-signatures to glycocodes

    B. M. Sattelle and A. Almond, Phys. Chem. Chem. Phys., 2012, 14, 5843
    DOI: 10.1039/C2CP40071E

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